Acta Crystallographica Section D

Biological Crystallography

Volume 68, Part 9 (September 2012)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Lid-loop motion in the active site of alginate lyase A1-III. The lid loop (residues 64-85) moves from an open to a closed form to make interactions with a bound substrate (spheres) and a catalytic Tyr residue (p. 1207).

research papers


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Acta Cryst. (2012). D68, 1071-1076  [ doi:10.1107/S0907444912019932 ]

Structural features of the single-stranded DNA-binding protein MoSub1 from Magnaporthe oryzae

J. Huang, Y. Zhao, D. Huang, H. Liu, N. Justin, W. Zhao, J. Liu and Y. Peng

Synopsis: The crystal structure of MoSub1, a Sub1/PC4 orthologue from rice blast fungus, has two novel features N-terminal and C-terminal to the DNA-binding domain. It has a similar dimer interface and DNA-binding region to PC4 and the protein binds single-stranded DNA tightly.

PDB reference: 4agh

Online 18 August 2012


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Acta Cryst. (2012). D68, 1077-1087  [ doi:10.1107/S0907444912020100 ]

On the variability of experimental data in macromolecular crystallography

E. Pozharski

Synopsis: Experimental errors in macromolecular crystallography are underestimated as they do not account for the contribution of crystal-to-crystal variations.

Online 18 August 2012


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Acta Cryst. (2012). D68, 1088-1097  [ doi:10.1107/S0907444912020598 ]

Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670

S. Pletnev, N. V. Pletneva, E. A. Souslova, D. M. Chudakov, S. Lukyanov, A. Wlodawer, Z. Dauter and V. Pletnev

Synopsis: The crystal structures of the far-red fluorescent proteins eqFP650 and eqFP670 have been solved at 1.8 and 1.6 Å resolution, respectively. This permitted identification of the structural elements responsible for the bathochromic shift in both considered far-red fluorescent proteins.

PDB references: 4edo and 4eds

Online 18 August 2012


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Acta Cryst. (2012). D68, 1098-1107  [ doi:10.1107/S090744491202094X ]

Structural and functional studies of ReP1-NCXSQ, a protein regulating the squid nerve Na+/Ca2+ exchanger

A. Cousido-Siah, D. Ayoub, G. Berberián, M. Bollo, A. Van Dorsselaer, F. Debaene, R. DiPolo, T. Petrova, C. Schulze-Briese, V. Olieric, A. Esteves, A. Mitschler, S. Sanglier-Cianférani, L. Beaugé and A. Podjarny

Synopsis: Structural and functional studies show the importance of palmitic acid transport by the cytosolic protein ReP1-NCXSQ in regulation of the squid nerve Na+/Ca2+ exchanger NCXSQ1.

PDB references: 3ppt and 3pp6

Online 18 August 2012


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Acta Cryst. (2012). D68, 1108-1117  [ doi:10.1107/S0907444912021361 ]

Spatial distribution of radiation damage to crystalline proteins at 25-300 K

M. Warkentin, R. Badeau, J. B. Hopkins and R. E. Thorne

Synopsis: Dose-dependent atomic B factors are used to determine the average spatial distribution of radiation damage to crystalline thaumatin and urease.

PDB references: 4ek0, 4eka, 4ekb, 4ekh, 4eko, 4ekt, 4el2, 4el3, 4el7, 4ela, 4ep8, 4epb, 4epd and 4epe

Online 18 August 2012


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Acta Cryst. (2012). D68, 1118-1127  [ doi:10.1107/S0907444912021269 ]

Detection of alternative conformations by unrestrained refinement

O. V. Sobolev and V. Y. Lunin

Synopsis: The values of atomic shifts in unrestrained refinement can hint at alternative conformations.

Online 18 August 2012


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Acta Cryst. (2012). D68, 1128-1133  [ doi:10.1107/S0907444912022561 ]

The structure of augmenter of liver regeneration crystallized in the presence of 50 mM CdCl2 reveals a novel Cd2Cl4O6 cluster that aids in crystal packing

Q. Florence, C.-K. Wu, J. Habel, J. T. Swindell, B.-C. Wang and J. P. Rose

Synopsis: The 2.4 Å crystal structure of the protein augmenter of liver regeneration (hsALR) containing a 14-residue histidine purification tag has been determined by Cd-SAD. The structure reveals a tetramer (two hsALR homodimers) bridged by a novel Cd2Cl4O6 cluster that produces a crystal packing environment that can better accommodate the N-terminal purification tag.

PDB reference: 3r7c

Online 18 August 2012


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Acta Cryst. (2012). D68, 1134-1139  [ doi:10.1107/S0907444912023141 ]

Structure of Escherichia coli BamB and its interaction with POTRA domains of BamA

C. Dong, X. Yang, H.-F. Hou, Y.-Q. Shen and Y.-H. Dong

Synopsis: The BAM complex is comprised of an integral [beta]-barrel outer membrane protein BamA and four accessory lipoproteins BamB, BamC, BamD and BamE. Here, the crystal structure of BamB is reported.

PDB reference: 3q54

Online 18 August 2012


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Acta Cryst. (2012). D68, 1140-1151  [ doi:10.1107/S0907444912021555 ]

High-resolution structure of Bombyx mori lipoprotein 7: crystallographic determination of the identity of the protein and its potential role in detoxification

A. J. Pietrzyk, S. Panjikar, A. Bujacz, J. Mueller-Dieckmann, M. Lochynska, M. Jaskolski and G. Bujacz

Synopsis: Three crystal structures of a lipoprotein (Bmlp7) of unknown function, a member of the 30 kDa lipoprotein family from mulberry silkworm (B. mori L.) haemolymph, have been determined. The haemolymph-isolated protein was identified through successful sequence assignment according to electron-density maps at 1.33 Å resolution.

PDB references: 4efp, 4efq and 4efr

Online 18 August 2012


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Acta Cryst. (2012). D68, 1152-1162  [ doi:10.1107/S0907444912023475 ]

Segmenting data sets for RIP

D. de Sanctis and M. H. Nanao

Synopsis: A method for experimental phasing by segmenting a large data set into sub-data sets for radiation-damage-induced phasing is presented.

Online 18 August 2012


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Acta Cryst. (2012). D68, 1163-1174  [ doi:10.1107/S0907444912022834 ]

Structure of a tetrameric galectin from Cinachyrella sp. (ball sponge)

D. M. Freymann, Y. Nakamura, P. J. Focia, R. Sakai and G. T. Swanson

Synopsis: The structure of a tetrameric sponge galectin suggests a basis for glutamate receptor potentiation.

PDB references: 4agr, 4agv and 4agg

Online 18 August 2012


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Acta Cryst. (2012). D68, 1175-1188  [ doi:10.1107/S0907444912022640 ]

Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus

T. Matsui, J. Yamane, N. Mogi, H. Yamaguchi, H. Takemoto, M. Yao and I. Tanaka

Synopsis: Structures of FtsZ from S. aureus in apo, GDP-bound and PC190723-complex forms are reported; FtsZ undergoes distinct conformational changes. These structural features are discussed and related to the crucial functions of FtsZ.

PDB references: 3vo8, 3vo9, 3vpa, 3voa and 3vob

Online 18 August 2012


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Acta Cryst. (2012). D68, 1189-1193  [ doi:10.1107/S0907444912024080 ]

Structural analysis of the Asn152Gly mutant of P99 cephalosporinase

J. F. Ruble, S. T. Lefurgy, V. W. Cornish and R. A. Powers

Synopsis: P99 cephalosporinase is a class C [beta]-lactamase that is responsible in part for the widespread bacterial resistance to [beta]-lactam antibiotics. Here, the X-ray crystal structure of the apo Asn152Gly mutant of P99 has been determined to 1.95 Å resolution.

PDB reference: 3s4x

Online 18 August 2012


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Acta Cryst. (2012). D68, 1194-1200  [ doi:10.1107/S0907444912024699 ]

Structure of the prolyl-tRNA synthetase from the eukaryotic pathogen Giardia lamblia

E. T. Larson, J. E. Kim, A. J. Napuli, C. L. M. J. Verlinde, E. Fan, F. H. Zucker, W. C. Van Voorhis, F. S. Buckner, W. G. J. Hol and E. A. Merritt

Synopsis: The structure of Giardia prolyl-tRNA synthetase cocrystallized with proline and ATP shows evidence for half-of-the-sites activity, leading to a corresponding mixture of reaction substrates and product (prolyl-AMP) in the two active sites of the dimer.

PDB reference: 3ial

Online 18 August 2012


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Acta Cryst. (2012). D68, 1201-1206  [ doi:10.1107/S0907444912024808 ]

Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography

A. Kovalevsky, B. L. Hanson, S. A. Mason, V. T. Forsyth, Z. Fisher, M. Mustyakimov, M. P. Blakeley, D. A. Keen and P. Langan

Synopsis: A joint X-ray/neutron structure of D-xylose isomerase in complex with the inhibitor sorbitol was determined at room temperature at an acidic pH of 5.9. Protonation of the O5 O atom of the sugar was directly observed in the nuclear density maps. Under acidic conditions sorbitol gains a water-mediated interaction with the enzyme active site, which may explain the increased potency of the inhibitor at low pH.

PDB references: 4duo and 4dvo

Online 18 August 2012


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Acta Cryst. (2012). D68, 1207-1216  [ doi:10.1107/S090744491202495X ]

Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III

B. Mikami, M. Ban, S. Suzuki, H.-J. Yoon, O. Miyake, M. Yamasaki, K. Ogura, Y. Maruyama, W. Hashimoto and K. Murata

Synopsis: The structures of apo and holo mutants of alginate lyase A1-III revealed a large open/closed conformational change of lid loop. The closed lid loop is involved both in the binding of substrate and catalysis of the enzyme.

PDB references: 4e1y, 4f10 and 4f13

Online 18 August 2012


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Acta Cryst. (2012). D68, 1217-1222  [ doi:10.1107/S0907444912025772 ]

Structure determination of enterovirus 71

P. Plevka, R. Perera, J. Cardosa, R. J. Kuhn and M. G. Rossmann

Synopsis: Determination of the orientation of the enterovirus 71 virions in the crystal required the calculation of a locked rotation function that included only icosahedral threefold and fivefold symmetry axes. Otherwise, misleading high rotation-function values were produced by accidental alignment of icosahedral and crystallographic twofold axes.

PDB reference: 4aed

Online 18 August 2012


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Acta Cryst. (2012). D68, 1223-1231  [ doi:10.1107/S0907444912026054 ]

Analysis of copper-ligand bond lengths in X-ray structures of different types of copper sites in proteins

L. A. Abriata

Synopsis: An updated picture of the ligand sets and copper-ligand atom bond lengths in proteins is presented.

Online 18 August 2012


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Acta Cryst. (2012). D68, 1232-1241  [ doi:10.1107/S0907444912026236 ]

The structure of Enterococcus faecalis thymidylate synthase provides clues about folate bacterial metabolism

C. Pozzi, S. Ferrari, D. Cortesi, R. Luciani, R. M. Stroud, A. Catalano, M. P. Costi and S. Mangani

Synopsis: The crystal structure of thymidylate synthase from E. faecalis was obtained as a native complex with 5-formyltetrahydrofolate (5-FTHF). The structure supports the role of 5-FTHF, which is naturally present in the bacterial cell, as a storage form of the folate metabolite and as an enzyme regulator.

PDB reference: 3uwl

Online 18 August 2012


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Acta Cryst. (2012). D68, 1242-1252  [ doi:10.1107/S0907444912026212 ]

Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal

J.-Y. Zhu, Z.-Q. Fu, L. Chen, H. Xu, J. Chrzas, J. Rose and B.-C. Wang

Synopsis: The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using data collected from a moderately diffracting crystal and 1.9 Å synchrotron X-rays.

PDB references: 3o3k and 3ov8

Online 18 August 2012


short communications


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Acta Cryst. (2012). D68, 1253-1258  [ doi:10.1107/S0907444912024420 ]

Experimental phasing using zinc anomalous scattering

S.-S. Cha, Y. J. An, C.-S. Jeong, M.-K. Kim, S.-G. Lee, K.-H. Lee and B.-H. Oh

Synopsis: The surface of proteins can be charged with zinc ions and the anomalous signals from these zinc ions can be used for structure determination of proteins.

PDB references: 4dt3 and 4fc5

Online 18 August 2012


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